diff --git a/NAMESPACE b/NAMESPACE index f2c5e8ce85978546608185ac4563c9f6a7019e2c..36d0c1d6f5333a6d0fdd3c431298200b9a2d0aac 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,10 +2,10 @@ export(ecxsys) export(lc) +export(multi_tox) export(plot_stress) export(plot_survival) export(predict_ecxsys) -export(predict_mixture) export(stress_to_survival) export(survival_to_stress) import(grDevices) diff --git a/NEWS.md b/NEWS.md index 07a6145365e9a17d10ee0188f14b69695e072973..17d92ed88803e7acc6ce12a90ad2489bbb89efba 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ * Rename all instances of "effect" to "survival". * Rename all instances of "ec" to "lc". +* Rename `predict_mixture()` to `multi_tox()`. # stressaddition 2.7.0 diff --git a/R/predict_mixture.R b/R/predict_mixture.R index a275ece3b18fe571da360959b5fecbefa2a8e668..3a9bab1f164e7761b88a3f03e75d426ad79ab2c1 100644 --- a/R/predict_mixture.R +++ b/R/predict_mixture.R @@ -54,7 +54,7 @@ #' survival_tox_observed = c(26, 25, 24, 27, 5, 0), #' survival_max = 30 #' ) -#' predict_mixture( +#' multi_tox( #' toxicant_a , #' toxicant_b , #' c(0, 0.02, 0.2, 2, 20), @@ -65,17 +65,17 @@ #' conc_a <- c(0, 0.03, 0.3, 3) #' conc_b <- 5.5 #' prop_ca <- 0.75 -#' mix_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca) -#' mix_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca) +#' mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca) +#' mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca) #' identical(mix_a$survival, mix_b$survival) #' #' @export -predict_mixture <- function(model_a, - model_b, - concentration_a, - concentration_b, - proportion_ca = 0.5, - survival_max = 100) { +multi_tox <- function(model_a, + model_b, + concentration_a, + concentration_b, + proportion_ca = 0.5, + survival_max = 100) { stopifnot( inherits(model_a, "ecxsys"), inherits(model_b, "ecxsys"), diff --git a/man/predict_mixture.Rd b/man/multi_tox.Rd similarity index 90% rename from man/predict_mixture.Rd rename to man/multi_tox.Rd index b15f7f1499ce7c6efb847f1e708078c5a8e2bfae..f518529eeab8103140c199db26eb9529f74057ff 100644 --- a/man/predict_mixture.Rd +++ b/man/multi_tox.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/predict_mixture.R -\name{predict_mixture} -\alias{predict_mixture} +\name{multi_tox} +\alias{multi_tox} \title{Predict the survival of a mixture of two toxicants} \usage{ -predict_mixture( +multi_tox( model_a, model_b, concentration_a, @@ -56,7 +56,7 @@ toxicant_b <- ecxsys( survival_tox_observed = c(26, 25, 24, 27, 5, 0), survival_max = 30 ) -predict_mixture( +multi_tox( toxicant_a , toxicant_b , c(0, 0.02, 0.2, 2, 20), @@ -67,8 +67,8 @@ predict_mixture( conc_a <- c(0, 0.03, 0.3, 3) conc_b <- 5.5 prop_ca <- 0.75 -mix_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca) -mix_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca) +mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca) +mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca) identical(mix_a$survival, mix_b$survival) } diff --git a/tests/testthat/test-predict_mixture.R b/tests/testthat/test-predict_mixture.R index cbc035a34afdd9164c3084fff70e428938ae2b28..77bf217d5bbb61c87ce08577f3b516a3840cde5b 100644 --- a/tests/testthat/test-predict_mixture.R +++ b/tests/testthat/test-predict_mixture.R @@ -34,7 +34,7 @@ model_b <- ecxsys( test_that("results have not changed", { # one concentration_b - new <- predict_mixture( + new <- multi_tox( model_a, model_b, c(0, 0.01, 0.1, 1, 7, 15), @@ -54,7 +54,7 @@ test_that("results have not changed", { expect_equal(new, reference, tolerance = 1e-5) # diverse concentration_b - new <- predict_mixture( + new <- multi_tox( model_a, model_b, c(0, 0.01, 0.1, 1, 7, 15), @@ -74,7 +74,7 @@ test_that("results have not changed", { expect_equal(new, reference, tolerance = 1e-5) # diverse concentration_b and custom survival_max - new <- predict_mixture( + new <- multi_tox( model_a, model_b, c(0, 0.01, 0.1, 1, 7, 15), @@ -100,8 +100,8 @@ test_that("predictions are symmetric", { conc_a <- c(0, 10^seq(log10(0.001), log10(40), length.out = 50)) conc_b <- 3.5 prop_ca <- 0.8 - survival_12 <- predict_mixture(model_a, model_b, conc_a, conc_b, prop_ca)$survival - survival_21 <- predict_mixture(model_b, model_a, conc_b, conc_a, prop_ca)$survival + survival_12 <- multi_tox(model_a, model_b, conc_a, conc_b, prop_ca)$survival + survival_21 <- multi_tox(model_b, model_a, conc_b, conc_a, prop_ca)$survival expect_equal(survival_12, survival_21) })